@jbrowse/plugin-wiggle 2.0.0 → 2.1.2

package/dist/index.js

@@ -1,19 +1,4 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -44,135 +29,99 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.YSCALEBAR_LABEL_OFFSET = exports.Tooltip = exports.linearWiggleDisplayModelFactory = exports.LinearWiggleDisplayReactComponent = exports.WiggleBaseRenderer = exports.WiggleRendering = void 0;
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-var WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
+exports.linearWiggleDisplayModelFactory = exports.WiggleBaseRenderer = exports.WiggleRendering = exports.Tooltip = exports.LinearWiggleDisplayReactComponent = void 0;
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+// locals
+const WiggleBaseRenderer_1 = __importDefault(require("./WiggleBaseRenderer"));
 exports.WiggleBaseRenderer = WiggleBaseRenderer_1.default;
-var WiggleRendering_1 = __importDefault(require("./WiggleRendering"));
+const WiggleRendering_1 = __importDefault(require("./WiggleRendering"));
 exports.WiggleRendering = WiggleRendering_1.default;
-var BigWigAdapter_1 = require("./BigWigAdapter");
-var DensityRenderer_1 = __importStar(require("./DensityRenderer"));
-var utils = __importStar(require("./util"));
-var LinearWiggleDisplay_1 = require("./LinearWiggleDisplay");
-Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_1.modelFactory; } });
-Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_1.ReactComponent; } });
-Object.defineProperty(exports, "YSCALEBAR_LABEL_OFFSET", { enumerable: true, get: function () { return LinearWiggleDisplay_1.YSCALEBAR_LABEL_OFFSET; } });
-var XYPlotRenderer_1 = __importStar(require("./XYPlotRenderer"));
-var LinePlotRenderer_1 = __importStar(require("./LinePlotRenderer"));
-var rpcMethods_1 = require("./WiggleRPC/rpcMethods");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var WigglePlugin = /** @class */ (function (_super) {
-    __extends(WigglePlugin, _super);
-    function WigglePlugin() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'WigglePlugin';
-        _this.exports = {
-            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_1.ReactComponent,
-            XYPlotRendererReactComponent: XYPlotRenderer_1.ReactComponent,
-            XYPlotRenderer: XYPlotRenderer_1.default,
-            xyPlotRendererConfigSchema: XYPlotRenderer_1.configSchema,
-            utils: utils,
+const BigWigAdapter_1 = __importDefault(require("./BigWigAdapter"));
+const QuantitativeTrack_1 = __importDefault(require("./QuantitativeTrack"));
+const MultiQuantitativeTrack_1 = __importDefault(require("./MultiQuantitativeTrack"));
+const MultiWiggleAdapter_1 = __importDefault(require("./MultiWiggleAdapter"));
+const DensityRenderer_1 = __importDefault(require("./DensityRenderer"));
+const XYPlotRenderer_1 = __importDefault(require("./XYPlotRenderer"));
+const LinePlotRenderer_1 = __importDefault(require("./LinePlotRenderer"));
+const LinearWiggleDisplay_1 = __importDefault(require("./LinearWiggleDisplay"));
+const MultiLinearWiggleDisplay_1 = __importDefault(require("./MultiLinearWiggleDisplay"));
+const MultiXYPlotRenderer_1 = __importDefault(require("./MultiXYPlotRenderer"));
+const MultiRowXYPlotRenderer_1 = __importDefault(require("./MultiRowXYPlotRenderer"));
+const MultiDensityRenderer_1 = __importDefault(require("./MultiDensityRenderer"));
+const MultiLineRenderer_1 = __importDefault(require("./MultiLineRenderer"));
+const MultiRowLineRenderer_1 = __importDefault(require("./MultiRowLineRenderer"));
+const CreateMultiWiggleExtension_1 = __importDefault(require("./CreateMultiWiggleExtension"));
+const MultiWiggleAddTrackWidget_1 = __importDefault(require("./MultiWiggleAddTrackWidget"));
+const utils = __importStar(require("./util"));
+const rpcMethods_1 = require("./WiggleRPC/rpcMethods");
+const LinearWiggleDisplay_2 = require("./LinearWiggleDisplay");
+Object.defineProperty(exports, "LinearWiggleDisplayReactComponent", { enumerable: true, get: function () { return LinearWiggleDisplay_2.ReactComponent; } });
+Object.defineProperty(exports, "linearWiggleDisplayModelFactory", { enumerable: true, get: function () { return LinearWiggleDisplay_2.modelFactory; } });
+Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return LinearWiggleDisplay_2.Tooltip; } });
+const XYPlotRenderer_2 = require("./XYPlotRenderer");
+class WigglePlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'WigglePlugin';
+        this.exports = {
+            LinearWiggleDisplayReactComponent: LinearWiggleDisplay_2.ReactComponent,
+            XYPlotRendererReactComponent: XYPlotRenderer_2.ReactComponent,
+            XYPlotRenderer: XYPlotRenderer_2.XYPlotRenderer,
             WiggleBaseRenderer: WiggleBaseRenderer_1.default,
-            linearWiggleDisplayModelFactory: LinearWiggleDisplay_1.modelFactory,
+            xyPlotRendererConfigSchema: XYPlotRenderer_2.configSchema,
+            utils,
+            linearWiggleDisplayModelFactory: LinearWiggleDisplay_2.modelFactory,
         };
-        return _this;
     }
-    WigglePlugin.prototype.install = function (pluginManager) {
-        pluginManager.addTrackType(function () {
-            var configSchema = (0, configuration_1.ConfigurationSchema)('QuantitativeTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
-            return new TrackType_1.default({
-                name: 'QuantitativeTrack',
-                configSchema: configSchema,
-                stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'QuantitativeTrack', configSchema),
-            });
-        });
-        pluginManager.addDisplayType(function () {
-            var configSchema = (0, LinearWiggleDisplay_1.configSchemaFactory)(pluginManager);
-            return new DisplayType_1.default({
-                name: 'LinearWiggleDisplay',
-                configSchema: configSchema,
-                stateModel: (0, LinearWiggleDisplay_1.modelFactory)(pluginManager, configSchema),
-                trackType: 'QuantitativeTrack',
-                viewType: 'LinearGenomeView',
-                ReactComponent: LinearWiggleDisplay_1.ReactComponent,
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'BigWigAdapter',
-                configSchema: BigWigAdapter_1.configSchema,
-                adapterCapabilities: [
-                    'hasResolution',
-                    'hasLocalStats',
-                    'hasGlobalStats',
-                ],
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./BigWigAdapter/BigWigAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.(bw|bigwig)$/i;
-                var adapterName = 'BigWigAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var obj = {
+    install(pm) {
+        (0, MultiWiggleAdapter_1.default)(pm);
+        (0, BigWigAdapter_1.default)(pm);
+        (0, QuantitativeTrack_1.default)(pm);
+        (0, MultiQuantitativeTrack_1.default)(pm);
+        (0, LinearWiggleDisplay_1.default)(pm);
+        (0, MultiLinearWiggleDisplay_1.default)(pm);
+        (0, LinePlotRenderer_1.default)(pm);
+        (0, XYPlotRenderer_1.default)(pm);
+        (0, DensityRenderer_1.default)(pm);
+        (0, MultiXYPlotRenderer_1.default)(pm);
+        (0, MultiRowXYPlotRenderer_1.default)(pm);
+        (0, MultiDensityRenderer_1.default)(pm);
+        (0, MultiLineRenderer_1.default)(pm);
+        (0, MultiRowLineRenderer_1.default)(pm);
+        (0, MultiWiggleAddTrackWidget_1.default)(pm);
+        (0, CreateMultiWiggleExtension_1.default)(pm);
+        pm.addToExtensionPoint('Core-guessAdapterForLocation', (cb) => {
+            return (file, index, hint) => {
+                const regexGuess = /\.(bw|bigwig)$/i;
+                const adapterName = 'BigWigAdapter';
+                const fileName = (0, tracks_1.getFileName)(file);
+                const obj = {
                     type: adapterName,
                     bigWigLocation: file,
                 };
-                if (regexGuess.test(fileName) && !adapterHint) {
+                if (regexGuess.test(fileName) && !hint) {
                     return obj;
                 }
-                else if (adapterHint === adapterName) {
+                else if (hint === adapterName) {
                     return obj;
                 }
-                return adapterGuesser(file, index, adapterHint);
+                return cb(file, index, hint);
             };
         });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-            return function (adapterName) {
+        pm.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
                 if (adapterName === 'BigWigAdapter') {
                     return 'QuantitativeTrack';
                 }
                 return trackTypeGuesser(adapterName);
             };
         });
-        pluginManager.addRendererType(function () {
-            return new DensityRenderer_1.default({
-                name: 'DensityRenderer',
-                ReactComponent: DensityRenderer_1.ReactComponent,
-                configSchema: DensityRenderer_1.configSchema,
-                pluginManager: pluginManager,
-            });
-        });
-        pluginManager.addRendererType(function () {
-            return new LinePlotRenderer_1.default({
-                name: 'LinePlotRenderer',
-                ReactComponent: LinePlotRenderer_1.ReactComponent,
-                configSchema: LinePlotRenderer_1.configSchema,
-                pluginManager: pluginManager,
-            });
-        });
-        pluginManager.addRendererType(function () {
-            return new XYPlotRenderer_1.default({
-                name: 'XYPlotRenderer',
-                ReactComponent: XYPlotRenderer_1.ReactComponent,
-                configSchema: XYPlotRenderer_1.configSchema,
-                pluginManager: pluginManager,
-            });
-        });
-        pluginManager.addRpcMethod(function () { return new rpcMethods_1.WiggleGetGlobalStats(pluginManager); });
-        pluginManager.addRpcMethod(function () { return new rpcMethods_1.WiggleGetMultiRegionStats(pluginManager); });
-    };
-    return WigglePlugin;
-}(Plugin_1.default));
+        pm.addRpcMethod(() => new rpcMethods_1.WiggleGetGlobalStats(pm));
+        pm.addRpcMethod(() => new rpcMethods_1.WiggleGetMultiRegionStats(pm));
+        pm.addRpcMethod(() => new rpcMethods_1.MultiWiggleGetSources(pm));
+    }
+}
 exports.default = WigglePlugin;
 __exportStar(require("./util"), exports);
-var Tooltip_1 = require("./LinearWiggleDisplay/components/Tooltip");
-Object.defineProperty(exports, "Tooltip", { enumerable: true, get: function () { return Tooltip_1.Tooltip; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAGzC,sDAIkC;AAElC,SAAS;AACT,8EAAqD;AAqHnD,6BArHK,4BAAkB,CAqHL;AApHpB,wEAA+C;AAmH7C,0BAnHK,yBAAe,CAmHL;AAlHjB,oEAA4C;AAC5C,4EAAoD;AACpD,sFAA8D;AAC9D,8EAAsD;AACtD,wEAAgD;AAChD,sEAA8C;AAC9C,0EAAkD;AAClD,gFAAwD;AACxD,0FAAkE;AAClE,gFAAwD;AACxD,sFAA8D;AAC9D,kFAA0D;AAC1D,4EAAoD;AACpD,kFAA0D;AAC1D,8FAAsE;AACtE,4FAAoE;AAEpE,8CAA+B;AAE/B,uDAI+B;AAE/B,+DAI8B;AAmF5B,kHAtFkB,oCAAiC,OAsFlB;AAIjC,gHAzFgB,kCAA+B,OAyFhB;AAH/B,wFArFA,6BAAO,OAqFA;AAlFT,qDAIyB;AAEzB,MAAqB,YAAa,SAAQ,gBAAM;IAAhD;;QACE,SAAI,GAAG,cAAc,CAAA;QA2DrB,YAAO,GAAG;YACR,iCAAiC,EAAjC,oCAAiC;YACjC,4BAA4B,EAA5B,+BAA4B;YAC5B,cAAc,EAAd,+BAAc;YACd,kBAAkB,EAAlB,4BAAkB;YAElB,0BAA0B,EAA1B,6BAA0B;YAC1B,KAAK;YACL,+BAA+B,EAA/B,kCAA+B;SAChC,CAAA;IACH,CAAC;IAnEC,OAAO,CAAC,EAAiB;QACvB,IAAA,4BAAmB,EAAC,EAAE,CAAC,CAAA;QACvB,IAAA,uBAAc,EAAC,EAAE,CAAC,CAAA;QAClB,IAAA,2BAAkB,EAAC,EAAE,CAAC,CAAA;QACtB,IAAA,gCAAuB,EAAC,EAAE,CAAC,CAAA;QAC3B,IAAA,6BAAoB,EAAC,EAAE,CAAC,CAAA;QACxB,IAAA,kCAAyB,EAAC,EAAE,CAAC,CAAA;QAC7B,IAAA,0BAAiB,EAAC,EAAE,CAAC,CAAA;QACrB,IAAA,wBAAe,EAAC,EAAE,CAAC,CAAA;QACnB,IAAA,yBAAgB,EAAC,EAAE,CAAC,CAAA;QACpB,IAAA,6BAAoB,EAAC,EAAE,CAAC,CAAA;QACxB,IAAA,gCAAuB,EAAC,EAAE,CAAC,CAAA;QAC3B,IAAA,8BAAqB,EAAC,EAAE,CAAC,CAAA;QACzB,IAAA,2BAAkB,EAAC,EAAE,CAAC,CAAA;QACtB,IAAA,8BAAqB,EAAC,EAAE,CAAC,CAAA;QACzB,IAAA,mCAA0B,EAAC,EAAE,CAAC,CAAA;QAC9B,IAAA,oCAA2B,EAAC,EAAE,CAAC,CAAA;QAE/B,EAAE,CAAC,mBAAmB,CACpB,8BAA8B,EAC9B,CAAC,EAAkB,EAAE,EAAE;YACrB,OAAO,CAAC,IAAkB,EAAE,KAAoB,EAAE,IAAa,EAAE,EAAE;gBACjE,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,eAAe,CAAA;gBACnC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,cAAc,EAAE,IAAI;iBACrB,CAAA;gBAED,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,IAAI,KAAK,WAAW,EAAE;oBAC/B,OAAO,GAAG,CAAA;iBACX;gBAED,OAAO,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;YAC9B,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,EAAE,CAAC,mBAAmB,CACpB,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,eAAe,EAAE;oBACnC,OAAO,mBAAmB,CAAA;iBAC3B;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,iCAAoB,CAAC,EAAE,CAAC,CAAC,CAAA;QACnD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,sCAAyB,CAAC,EAAE,CAAC,CAAC,CAAA;QACxD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,kCAAqB,CAAC,EAAE,CAAC,CAAC,CAAA;IACtD,CAAC;CAYF;AAtED,+BAsEC;AAED,yCAAsB"}

package/dist/util.d.ts

@@ -1,3 +1,6 @@
+import { FeatureStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare const YSCALEBAR_LABEL_OFFSET = 5;
 export interface ScaleOpts {
     domain: number[];
     range: number[];
@@ -5,6 +8,11 @@ export interface ScaleOpts {
     pivotValue?: number;
     inverted: boolean;
 }
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+}
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -16,7 +24,7 @@ export interface ScaleOpts {
  *   - pivotValue (number)
  *   - inverted (boolean)
  */
-export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number> | import("d3-scale").ScaleQuantize<number>;
+export declare function getScale({ domain, range, scaleType, pivotValue, inverted, }: ScaleOpts): import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
 /**
  * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0
  *
@@ -39,3 +47,28 @@ export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     domain: number[];
     bounds: number[];
 }): [number, number];
+export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
+    [key: string]: T[];
+};
+export declare function getStats(self: {
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}, opts: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<FeatureStats>;
+export declare function statsAutorun(self: {
+    estimatedStatsReady: boolean;
+    regionTooLarge: boolean;
+    setLoading: (aborter: AbortController) => void;
+    setError: (error: unknown) => void;
+    updateStats: (stats: FeatureStats, statsRegion: string) => void;
+    renderProps: () => Record<string, unknown>;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}): void;
+export declare function toP(s?: number): number;
+export declare function round(value: number): number;

package/dist/util.js

@@ -1,23 +1,13 @@
 "use strict";
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNiceDomain = exports.getOrigin = exports.getScale = void 0;
-var d3_scale_1 = require("d3-scale");
+exports.round = exports.toP = exports.statsAutorun = exports.getStats = exports.groupBy = exports.getNiceDomain = exports.getOrigin = exports.getScale = exports.YSCALEBAR_LABEL_OFFSET = void 0;
+const d3_scale_1 = require("d3-scale");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
+exports.YSCALEBAR_LABEL_OFFSET = 5;
 /**
  * produces a d3-scale from arguments. applies a "nice domain" adjustment
  *
@@ -29,10 +19,9 @@ var d3_scale_1 = require("d3-scale");
  *   - pivotValue (number)
  *   - inverted (boolean)
  */
-function getScale(_a) {
-    var _b = _a.domain, domain = _b === void 0 ? [] : _b, _c = _a.range, range = _c === void 0 ? [] : _c, scaleType = _a.scaleType, pivotValue = _a.pivotValue, inverted = _a.inverted;
-    var scale;
-    var _d = __read(domain, 2), min = _d[0], max = _d[1];
+function getScale({ domain = [], range = [], scaleType, pivotValue, inverted, }) {
+    let scale;
+    const [min, max] = domain;
     if (min === undefined || max === undefined) {
         throw new Error('invalid domain');
     }
@@ -51,7 +40,7 @@ function getScale(_a) {
     }
     scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max]);
     scale.nice();
-    var _e = __read(range, 2), rangeMin = _e[0], rangeMax = _e[1];
+    const [rangeMin, rangeMax] = range;
     if (rangeMin === undefined || rangeMax === undefined) {
         throw new Error('invalid range');
     }
@@ -94,10 +83,9 @@ exports.getOrigin = getOrigin;
  *   - stddev
  *   - scaleType (linear or log)
  */
-function getNiceDomain(_a) {
-    var scaleType = _a.scaleType, domain = _a.domain, bounds = _a.bounds;
-    var _b = __read(bounds, 2), minScore = _b[0], maxScore = _b[1];
-    var _c = __read(domain, 2), min = _c[0], max = _c[1];
+function getNiceDomain({ scaleType, domain, bounds, }) {
+    const [minScore, maxScore] = bounds;
+    let [min, max] = domain;
     if (scaleType === 'linear') {
         if (max < 0) {
             max = 0;
@@ -124,24 +112,131 @@ function getNiceDomain(_a) {
     if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {
         max = maxScore;
     }
-    var getScaleType = function (type) {
+    const getScaleType = (type) => {
         if (type === 'linear') {
             return (0, d3_scale_1.scaleLinear)();
         }
         if (type === 'log') {
-            var scale_1 = (0, d3_scale_1.scaleLog)();
-            scale_1.base(2);
-            return scale_1;
+            const scale = (0, d3_scale_1.scaleLog)();
+            scale.base(2);
+            return scale;
         }
         if (type === 'quantize') {
             return (0, d3_scale_1.scaleQuantize)();
         }
-        throw new Error("undefined scaleType ".concat(type));
+        throw new Error(`undefined scaleType ${type}`);
     };
-    var scale = getScaleType(scaleType);
+    const scale = getScaleType(scaleType);
     scale.domain([min, max]);
     scale.nice();
     return scale.domain();
 }
 exports.getNiceDomain = getNiceDomain;
+function groupBy(array, predicate) {
+    return array.reduce((acc, value) => {
+        var _a;
+        const entry = (acc[_a = predicate(value)] || (acc[_a] = []));
+        entry.push(value);
+        return acc;
+    }, {});
+}
+exports.groupBy = groupBy;
+async function getStats(self, opts) {
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const nd = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
+    const { adapterConfig, autoscaleType } = self;
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+    const params = {
+        sessionId,
+        adapterConfig,
+        statusCallback: (message) => {
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setMessage(message);
+            }
+        },
+        ...opts,
+    };
+    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
+        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalStats', params));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // globalsd uses heuristic to avoid unnecessary scoreMin<0
+        // if the scoreMin is never less than 0
+        // helps with most coverage bigwigs just being >0
+        return autoscaleType === 'globalsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
+                scoreMax: scoreMean + nd * scoreStdDev,
+            }
+            : results;
+    }
+    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
+        const { dynamicBlocks, bpPerPx } = (0, util_1.getContainingView)(self);
+        const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionStats', {
+            ...params,
+            regions: dynamicBlocks.contentBlocks.map(region => {
+                const { start, end } = region;
+                return {
+                    ...JSON.parse(JSON.stringify(region)),
+                    start: Math.floor(start),
+                    end: Math.ceil(end),
+                };
+            }),
+            bpPerPx,
+        }));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
+        // scoreMin is never less than 0 helps with most coverage bigwigs
+        // just being >0
+        return autoscaleType === 'localsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,
+                scoreMax: scoreMean + nd * scoreStdDev,
+            }
+            : results;
+    }
+    if (autoscaleType === 'zscale') {
+        return rpcManager.call(sessionId, 'WiggleGetGlobalStats', params);
+    }
+    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
+}
+exports.getStats = getStats;
+function statsAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            const aborter = new AbortController();
+            const view = (0, util_1.getContainingView)(self);
+            self.setLoading(aborter);
+            if (!view.initialized ||
+                !self.estimatedStatsReady ||
+                self.regionTooLarge) {
+                return;
+            }
+            const statsRegion = JSON.stringify(view.dynamicBlocks);
+            const wiggleStats = await getStats(self, {
+                signal: aborter.signal,
+                ...self.renderProps(),
+            });
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.updateStats(wiggleStats, statsRegion);
+            }
+        }
+        catch (e) {
+            if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
+                console.error(e);
+                self.setError(e);
+            }
+        }
+    }, { delay: 1000 }));
+}
+exports.statsAutorun = statsAutorun;
+function toP(s = 0) {
+    return +(+s).toPrecision(6);
+}
+exports.toP = toP;
+function round(value) {
+    return Math.round(value * 1e5) / 1e5;
+}
+exports.round = round;
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -1,17 +1,18 @@
+import { BigWig } from '@gmod/bbi';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { Feature } from '@jbrowse/core/util';
 interface WiggleOptions extends BaseOptions {
     resolution?: number;
 }
 export default class BigWigAdapter extends BaseFeatureDataAdapter {
-    private bigwig;
+    private setupP?;
     static capabilities: string[];
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    private setup;
+    private setupPre;
+    setup(opts?: BaseOptions): Promise<{
+        bigwig: BigWig;
+        header: any;
+    }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refIdToName(refId: number): Promise<any>;
     getGlobalStats(opts?: BaseOptions): Promise<import("@jbrowse/core/util/stats").FeatureStats>;